OK, I agree. That's not right. My gut tells me the problem is with the input jacks and/or V1. But since the pops occur on either channel the problem should be something common to both channels. Get a good set of voltage readings for the amp. And don't omit zero volt readings. They're important too.
Thanks sluckey. I know it's not right, I have built about ten tweeds including another 5F4 and it's the only one that does this. But I must admit, I had a hard time convincing you this one has something wrong...

Here's the voltage chart. I went for the most accurate readings possible. B+ is 390V and tubes are 6L6 (30w max dissipation). 70% of that max dissipation gives 21w. So I did 21/390 which gives 56mA. Tubes are biased 10mA below that at 46mA. I can't go above, I'm already up full on the bias pot (33K resistor soldered across it) and my B+ is already quite low I think since the original fender schematic shows a 410V B+... When I say (200mV) it means that the readings were taken with the MM set on the 200mV range.
Tube
Pin V1 V2 V3 V4 V5 V6
1 134 176 194.9 00.2(200mV) 0 125.2(200mV)
2 00.8(200mV) 5.6(200mV) 8.1(200mV) 3.38AC 3.38AC 405
3 2.1 1.25 1.53 388 387 00.5(200mV)
4 3.38AC 3.38AC 3.38AC 393 393 350AC
5 3.38AC 3.38AC 3.38AC -34.3 -34.5 0
6 130.4 270 260 -34.4 -34.5 350AC
7 3.3(200mV) 176 22.2 3.38AC 3.38AC 0
8 2.1 177.3 70.2 00.2(200mV) 0 406
9 3.38AC 3.38AC 3.38AC
Did you just build this amp? Has it ever worked right? Is this a customer's amp? What's the story?
Yes, I built this amp back in April. It worked well. I don't remember trying it with pedals though, but I think I did and obviously it didn't pop or I wouldn't have sent it. Its owner lives 400 miles away from me so I shipped it over to him and it worked well. Then I think about two months later he had to change the power tubes (NOS 5881s) because one of them failed. He also stated that the amp was making noise (probably the same kind of noise it makes today) and that pedals popped. He also told me that he inserted a preamp tube the wrong way and lit the amp with it...
That's when I told him to stop doing anything to it and to take it to a local tech. He did and the amp was actually returned to him with more noise and more pedal pops than before, which is when I asked him to return it to me...
He doesn't remember which preamp tube he mis-inserted...
I don't know more than this...